Research workbench
Kallikrein-related peptidase 8 leupeptin inhibitor complex
Analyse Kallikrein-related peptidase 8 leupeptin inhibitor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MS4
- Type
- protein
- Length
- 924 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kallikrein-8; Leupeptin
- EC
- 3.4.21.118
- UniProt
- O60259
- Ligands
- ACE, CA
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Kallikrein-8 (EC 3.4.21.118) | protein | 228 | 10% helix, 34% strand | O60259 |
| E, F, G, H | Leupeptin | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains A, E, B, F, C, G, D, H
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- TBU · Tertiary-butyl alcohol · additive · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.57 | 0.77 | 35 | empty |
| 2 | 396 | 0.55 | 0.74 | 42 | empty |
| 3 | 72 | 0.38 | 0.78 | 18 | empty |
| 4 | 66 | 0.36 | 0.78 | 18 | empty |
| 5 | 102 | 0.35 | 0.74 | 20 | TBU |
Interfaces
7 interfaces between chains.
- A–B · 675 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 599 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 581 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 424 Ų buried · 13 hydrogen bonds · protein-protein
- C–G · 399 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 4 covalent, 4 modified (disulfide, covalent ligand, nonstandard).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O60259
- Elsewhere: RCSB PDB 5MS4 · PDBe 5MS4 · UniProt O60259
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